The present invention relates to a method for creating physiologically active compounds useful for drugs, agricultural chemicals and the like by using computers.
In order to create useful drugs, agricultural chemicals and the like, it is essential to use a lead compound that has been already confirmed to have a desired physiological activity which should be a starting point of various chemical modifications. However, any logical method for creating a lead compound has not yet been known. Therefore, in general, physiologically active substances, e.g., hormones or nerve transmitter substances in a living body, or compounds that have already been confirmed to have a desired physiological activity by random screening are used as lead compounds.
On the other hand, three-dimensional structures of a lot of biopolymers have been already elucidated by X-ray crystallography, and many three-dimensional structures of complexes of a low molecular weight compound (ligand) such as an enzyme inhibitor and a biopolymer have also been reported. As a result, it has been revealed a natural rule that, in order to have a physiological activity, it is essential for a compound to fit the binding site of the biopolymer with good fitness and able to stably bind thereto. On the basis of these findings, it becomes possible to determine whether or not a compound exhibits physiological activity through binding to the biopolymer, i.e., whether or not the compound may possibly act as a ligand, by calculating the possibility of binding to the ligand binding site of the target biopolymer and the compound, strength of the binding and the like by means of computers. This method is paid much attention as means for rationally generating lead compounds, physiologically active compounds and the like.
As computersized methods for creating physiologically active compounds, there have been known a method of automatically constructing structures that are able to bind to the ligand-binding site of the biopolymer in an optimal condition (e.g., a condition that affords maximum hydrogen bond) by computation (automatic structure construction method), and a method of identifying compounds that satisfy requirements for having the physiological activity from databases of existing compounds (database method).
As the automatic structure construction method, the method of Nisibata et al. has been known (Nishibata, Y. and Itai, A, Tetrahedron, 47, pp.8985-8990, 1991; Nishibata, Y and Itai, A, J. Med. Chem, 36, pp.2921-2928, 1993). The advantage of the automatic structure construction method is that it can broadly suggest desirable structures that meet the requirements for exhibiting physiological activity regardless of known or unknown structures.
As the database method, there has been known a method of selecting compounds by judging whether or not types of functional groups, their relative three-dimensional positions and other in compounds correspond to those in a drug already known to bind to a biopolymer based on the structural information of the drug (for example, a method utilizing programs such as ISIS-3D:MDL Information Systems, Inc.; UNITY: Tripos, Inc.; and Chem-X: Chemical Design Ltd). This method can be utilized even when structural information of the target biopolymer is not available, and therefore, it can be used for a wide range of purposes.
When three-dimensional coordinates of the ligand-binding region of biopolymers are available, a more reliable database search method excluding any hypotheses and preconceptions can be utilized. The present inventors developed a method for automatically estimating the most stable complex structure of a biopolymer and a ligand (program xe2x80x9cADAMxe2x80x9d, PCT International Publication WO93/20525; Yamada, M. et al., J. Mol. Biol., 243, pp.310-326, 1994), and, by using this method, completed a method for identifying ligand compounds capable of stably binding to the ligand-binding region of a target biopolymer from a three-dimensional structure database (program xe2x80x9cADAMandEVExe2x80x9d, PCT International Publication WO96/13785; the 24th Symposium for Structure-Activity Relationship, Mizutani M et al., subject number 14S20, 1996). This method is characterized in that it enables high speed search of desired ligand compounds from a database based on energetic stability of complexes while not only considering degrees of freedom for binding modes and conformations but also optimizing torsion angles in a continuous space.
When the basic molecular skeleton of a ligand structure that has been confirmed or assumed to bind to the target biopolymer is available, a high-speed database search method based on the matching of topologies can be utilized program xe2x80x9cEUREKAxe2x80x9d, PCT/JP96/03325). In this method, derivatives that can bind to the ligand-binding region of the biopolymer or molecules having analogous structures (analogs) can be retrieved from a database based on the binding mode to the biopolymer and conformations of the basic molecular skeleton.
While the above database search method may be applied to a database composed of any compounds, it has an advantage that, by searching a database of available (in-house or commercially available) compounds, one can immediately obtain hit compounds satisfying the requirements and evaluate their biological activity without syntheses. When a database storing only existing (reported) compounds is used, the method has an advantage that the identified compounds may at least exist, and synthetic method and physicochemical properties thereof are often already known, although the compounds might not be immediately obtained without synthesis.
However, structures stored in such databases of available compounds or existing compounds constitute only a part of an astronomical number of structures that can theoretically exist, and the structures may sometimes be biased or they may exist sparsely among the possible structures. Therefore, they often do not contain any compounds with an optimum chemical structure endowing the maximum physiological activity in nature. When such a database is used and if retrieved compounds have physiological activity, there arise problems that truly promising compounds as lead compounds may be overlooked because of a weak activity of retrieved compounds, and that great effort and time may be needed for improving the retrieved compounds because of large deviation from the optimal structure.
When a certain structure has been known as a lead, or alternatively, a lead has been found by random screening or the aforementioned methods, improvement to achieve the highest desired physiological activity by chemical modification is conventionally performed by synthesizing a great number of derivatives and analogous compounds by trial-and-error, and therefore, it requires great efforts and time.
On the other hand, as an experimental method for efficient development of medicaments, a method comprising simultaneous synthesis or parallel screening of a large number of compounds consisting of those covering all possibilities of functional groups in natures and positions and structural units in connecting order and the like attracts much attention (combinatorial method). For example, a large number of compounds covering all combinations of substitutable positions present on a basic molecular skeleton and substituents, or all combinations of connecting order of two or more structural units like peptides are first generated, synthesized by parallel operations of several steps, and subjected all the compounds to an assay for the physiological activity at a time (Gallop, M A et al., J. Med. Chem., 37, pp.1233-1251, 1994: Burgess, K et al., J. Med. Chem., 37, pp.2985-2987, 1994). This method has an advantage that lead generation and optimization of the physiological activity can be done by the same procedure, because the most physiologically active compound with the basic molecular skeleton is readily selected from the generated combinations.
An object of the present invention is to provide a method for efficiently creating physiologically active compounds, wherein the aforementioned problems are solved by use of computers. More specifically, the object of the present invention is to identify compounds having structures suitable for the desired physiological activity through appropriate selection from generated compounds covering all possibilities in types or positions of functional groups to be added to a basic molecular skeleton, or in connecting order of various structural units.
The present inventors conducted various studies to develop a method for directly identifying an optimal structure as favorable as possible for a desired physiological activity without great trial-and-error efforts, and as a result, achieved the above object by combining a database construction method based on the concept of the above mentioned experimental combinatorial method and the database search method that has been developed by the present inventors. That is, the present inventors found that extremely efficient creation of physiologically active compounds can be performed by generating three-dimensional struck databases of compounds covering at combinations of substitutable positions and substituents for various basic molecular skeletons, or combinations of connecting order of structural units by computers, and searching the database by the above mentioned database search method. Because it becomes possible by employing this method to search a database containing an enormous number of compounds, which is completely impossible to be realized by the conventional combinatorial method utilizing chemical syntheses, compounds that may exhibit the maximum physiological activity can be identified by a single search. The present invention has been completed based on these findings.
The present invention thus provides a method for creating physiologically active compounds using computers, comprising the following steps: (1) generating a compound database storing molecular structures covering all the combinations of one or more substitution site selected from substitutable sites existing on a basic molecular skeleton and utilizable substituents; and (2) idetifying a molecular structure satisfying the requirements necessary for exhibiting the physiological activity from the compound database. As used herein, the term xe2x80x9cgeneration of physiological activity compoundxe2x80x9d should be construed to have its broadest meaning including concepts of creation and optimization of compounds having physiological activity such as creation of novel lead compounds, creation of novel lead compounds and optimization of the created lead compounds, and optimization of novel lead compounds utilizing molecular skeletons of already known ligand compounds.
In the step (1), any basic molecular skeletons may be used so long as structural modifications such as replacement, addition, or removal of substituents are possible. However, it is preferred to use the whole or a part of the basic structure of a ligand that has been already confirmed or is expected to have the desired biological activity, or a molecular structure which is not difficult to be synthesized or synthetically modified in its structure. Examples of the basic structure that has been already confirmed to have desired biological activity include benzodiazepine skeleton, barbiturate skeleton and the like. Examples of the basic structure that is expected to have the desired biological activity include those molecular structures created or selected by the methods utilizing xe2x80x9cLEGENDxe2x80x9d or xe2x80x9cADAMandEVExe2x80x9d. Examples of the molecular structure easy to be synthesized or synthetically modified in its structure include molecular skeletons created by connecting one or more structural units having modifiable sites and one or more connectors alternately. In this case, the basic molecular skeleton may be suitably selected from one or more molecular skeletons combinatorially generated from combinations of one or more structural units and connectors.
According to other embodiments of the present invention, there are provided three-dimensional databases used for the method of creating physiologically active compounds by database search methods using computers, which database stores molecular structures covering all the combinations of one or more substitution sites selected from substitutable sites existing on a basic molecular skeleton and utilizable substituents; and computer-readable media storing the database. The basic molecular skeleton used for generating molecular structures stored in the database may be any molecular skeletons for which structural modifications such as replacement, addition, or removal of substituents are possible. Specifically, those mentioned above can be used.